Is there a difference in doing Anaglyph 3D directly in blender instead of using other apps?
Ok after doing many test, it is absolutely better to render it directly from Blender itself. Mainly because you can control the convergence. 

If you do it in post (with the method described above) it will fake convergence and instead of giving depth to your objects it will give depth to the entire screen with a slight depth to the objects (when I have time I will post examples).

You can get a much deeper 3D effect if you set your convergence correctly and dividing the interocular distance by 30. 

So to recap if you can always render your Anaglyph images directly from Blender instead of faking the effect in post. 

EDIT:

For sake of completeness I will post the differences. Keep in mind you will need 3D glasses (red/cyan) to view the below pics. 

First is the 2D pic made into 3D from Photoshop (Cheat):



Second pic is Minimum convergence rendered directly out of Blender:



Last pic if Maximum Convergence directly out of Blender.



As you can see (if you had the glasses on) that doing it the cheat way gives you less depth than the minimum convergence. Although it still gives some. 

The maximum convergence you can clearly see the chair popping out of the screen. So this is the best route to go for Anaglyph. 

Keep in mind the maximum convergence will not always be best for your scene. It would depend on where you consider the middle, front and back of your scene. So don't always use maximum. I was just showing it as a reference.